AML datasets

Mouse datasets

Note: Validation mice also available via Haemdata/Ondrive. See X for more details.

First, we need to setup the pin-board and download the mouse datasets.

library(haemdata)
use_pinboard("devel")

all_mice <- get_pin("mmu_mrna_all_mice_GENCODEm28_HLT_qc.rds")

2016 mice

se <- subset(all_mice,
    select = grepl("2016", SummarizedExperiment::colData(all_mice)$batch)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2016")

2018 mice

se <- subset(all_mice,
    select = grepl("AML.mRNA.2018.all_samples", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2018")

Radiation mice

se <- subset(all_mice,
    select = grepl("AML.mRNA.2020", SummarizedExperiment::colData(all_mice)$cohort)
)
se <- subset(se,
    select = grepl("PBMC", SummarizedExperiment::colData(se)$tissue)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

metadata_mmu |>
plot_cohort_survival("AML.mRNA.2020")

Chemo mice

se <- subset(all_mice,
    select = grepl("RxGroup", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

metadata_mmu |>
plot_cohort_survival("RxGroup")

scRNAseq mice 2022

se <- subset(all_mice,
    select = grepl("AML.scRNAseq.2022", SummarizedExperiment::colData(all_mice)$cohort)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

Bone marrow

se <- subset(all_mice,
    select = ("BM" == SummarizedExperiment::colData(all_mice)$tissue)
)
se <- subset(se,
    select = grepl("AML", SummarizedExperiment::colData(se)$cohort)
)

pca <- pca_se(se)

pca$biplot

pca$pairs_plot

pca$correlation_plot

plot_transgenes_se(se)

Human datasets

First, we need to setup the pin-board from which well retrieve the human datasets

library(haemdata)
use_pinboard("devel")

COH patients

City of Hope Biobank FLT3 patients

Include some background info on these samples, IRB etc

library(haemdata)
use_pinboard("devel")
se <- get_pin("hsa_mrna_flt3_GENCODEr40_qc.rds")

# ## Add week_scaled column, where time is scaled for each patient
# SummarizedExperiment::colData(se) <- SummarizedExperiment::colData(se) |>
#     janitor::remove_constant() |>
#     dplyr::as_tibble() |>
#     dplyr::group_by(patient_id) |>
#     dplyr::mutate(weeks_scaled = as.vector(scale(weeks))) |>
#     dplyr::ungroup() |>
#     `rownames<-`(colnames(se)) |>
#     S4Vectors::DataFrame()

#pca <- pca_se(se, col_by = "weeks_scaled")
pca <- pca_se(se, col_by = "patient_id")

pca$biplot

pca$pairs_plot

pca$correlation_plot

Relapse patients

Kim et al 2020 Sci Rep

Bioproject: PRJEB27973

se <- get_pin("hsa_mrna_kim_GENCODEr40_qc.rds")

pca <- pca_se(se, col_by = "timepoint")

pca$biplot

pca$pairs_plot

pca$correlation_plot